By using bioinformatics tools different types of analysis of biological data can be done. Some of the analyses have been briefly discussed in this section.
(i) Processing Raw Information:
The biological information hidden in DNA/RNA and protein sequences is generated experimentally. These are called raw information.
Using bioinformatics tools these informations are processed into genes and proteins and a relationship is established between a gene and a protein. Phylogenetic relationships can also be established among the species of organisms.
Using bioinformatics tools such as GenMark (for bacteria), and GeneScan (for eukaryotes) gene prediction is carried out in organisms. GenScan can identify introns, exons, promotor sites and poly A signals and other gene identification algorithms.
By using computer programmes protein sequences can be deduced from the predicted genes.
(iv) Regulatory Sequences:
Using computer programmes the regulatory sequences can also be identified and analysed.
(v) Phylogenetic Relationships:
There are a few web-based applications that will allow you to carry out phylogenetic analysis over the web. By aligning multiple sequences, calculating evolutionary distance and constructing phylogenetic trees, you can establish phylogenetic relationship between two organisms.
Internet-based applications that provide phylogenetic analysis capabilities are WEBPHYLIP, Phylo BLAST, Gen Tree and BLAST2 & Orthologue Search Server. The cluster of orthologous groups (COGs) database simplifies the evolutionary studies of complete genomes and improves functional assignment of individual protein.
(vi) Reconstruction of Metabolic Pathways:
Reconstruction of metabolic pathways is one of the indispensable final steps of all genome analyses. It is also a convergence point for the data produced by different methods. The ENZYME database lists name and catalysed reaction for all the enzymes that have been assigned official Enzyme Commission (EC) numbers.
(vii) Prediction of Function of Unknown Genes:
By using the bioinformatics tools and databases, you can predict the function of unknown genes.